Tuesday, August 17, 2004

Your Genome is Smaller than Microsoft Office

How inspirational are the information systems of biology?

If we took your entire genetic code -- the entire biological program that resulted in your cells, organs, body and mind -- and burned it into a CD, it would be smaller than Microsoft Office. Two digital bits can encode for the four DNA bases (A,T,C and G) resulting in a 750MB file that can be compressed for the preponderance of structural filler in the DNA chain. Even with simple Huffman encoding, we should get below the 486MB of my minimal Office 2004 install.

If much of the human genome consists of vestigial evolutionary and parasitic remnants that serve no useful purpose, then we could compress it to 60MB of concentrated information.

What does this tell us about Microsoft? About software development? About complex systems development in general?

9 Comments:

I dont know about software development and Microsoft, something sure the Micro will disapear. Something sure is, Bill Gates will disapear too if he does not sign up for Cryonics. And venture capital might also disapear because I dont see any for profit corp beyond nanotechnology.

Very interesting observation Paul. It makes me want to think about a new post on quantum computational equivalence (blending Wolfram's notions with David Deutsch).

It also reminds me of the observation that the code might be compact, but just look at the compiler. (The ribosome is pretty amazing as a molecular assembler, by the way, weighing in at just 99K atoms)

Now, as to your post, do you literally mean "quantum" (e.g., Penrose's arguments about the brain) or just analog, non-linear and complex?

Much of the power in bio-processing comes from the leverage of feedback in the electrical, physical and chemical domains.

For example, in a fetus, the initial inter-neuronal connections, or "wiring" of the brain, follow chemical gradients. The massive number of inter-neuron connections in an adult brain could not be simply encoded in our DNA, even if the entire DNA sequence was dedicated to this one task. There are on the order of 100 trillion synaptic connections between 60 billion neurons in your brain.

This incredibly complex system is not 'installed' like Microsoft Office from your DNA. It is grown, first through widespread connectivity sprouting from 'static storms' of positive electro-chemical feedback, and then through the pruning of many underused connections through continuous usage-based feedback. In fact, at the age of 2 to 3 years old, humans hit their peak with a quadrillion synaptic connections, and twice the energy burn of an adult brain.

Very interesting point Steve. I think one point to be considered when comparing the human genome's information and MS Office is the differences in translating or compiling of the code. Due to the amazing capabilities of the central dogma, the genome's digital info can be translated into multiple possibilities. More basically, splice variants, cis/trans regulation and feedback regulation results in a more complex translation of the information to endpoint operations than a computer program on a PC. I just started blogging on VB and am fascinated by the ideas you and others have proposed. I will read you previous comments. A book I think you will find fascinating pulls together the ideas of quantum theory to biological systems.......Quantum Evolution by JohnJoe McFadden.

“The conference concluded with a Plenary Debate on the significance of quantum effects in biology. On the "Pro" side were physicist/author Paul Davies, experimentalist Anton Zeilinger, and me. Our opponents included Hans Frauenfelder, the protein dynamicist from Los Alamos. Paul gave compelling (in my view) arguments in favor of quantum biology, and Anton described quantum interference of porphyrin, a biological molecule.

I argued that protein dynamics, the engines of life, were controlled by quantum forces, specifically van der Waals London forces. Having spent years studying how anesthetic gases erase consciousness by the same London forces in non-polar pockets in critical brain proteins, I noted that high energy interactions in proteins cancel out, and weak but numerous, leveraged London forces reign.

Frauenfelder was having none of it. He said protein dynamics reflected purely solvent fluctuations; proteins were slaves! But his talk on myoglobin protein showed a xenon atom sitting in a non-polar pocket. He said the xenon inhibited the dynamics, but was of no biological significance. "But" I said, "xenon is an anesthetic, and binds only by quantum London forces. Your myoglobin has a quantum switch!" We lost the debate by audience vote of about 60% to 40%.”

Let's not forget though that human genes have had tens of thousands of years to evolve into an efficient and effective system (through survival of the fittest). MS-Office has only been around for just over a decade, and man-made in the first place. If software was subject to the same "survival of the fittest" requirement, I suspect that most software wouldn't have even made it on stores' shelves...

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For the daily blog, see flickr. Or get both with the RSS Feed from FeedburnerWhat is the J-Curve? The IRR curve over time for an early stage VC fund – that period of time in advance of mass-confirmation of a new idea. For fans of Kurzweil's curves and exponentials in general.